RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.JhjqpQ/RM_933210.WedNov130636122024 Search Engine = rmblast 2.13.0+ Threads = 32 Dependencies: TRF 4.09, RECON , RepeatScout 1.0.6, RepeatMasker 4.1.4 LTR Structural Analysis: Disabled [use -LTRStruct to enable] Random Number Seed: 1731508572 Database = /scratch/tmp/rModeler.JhjqpQ/GCA_039878825.1_bCotChi1.hap2 - Sequences = 191 - Bases = 966847183 - N50 = 105162541 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 171563393-183816686 | [ 1 ] 159310100-171563392 | [ ] 147056808-159310100 | [ ] 134803515-147056807 | [ 1 ] 122550223-134803515 | [ ] 110296930-122550222 | [ ] 98043637-110296929 | [ 1 ] 85790345-98043637 | [ 1 ] 73537052-85790344 | [ 1 ] 61283760-73537052 | [ ] 49030467-61283759 | [ 1 ] 36777174-49030466 | [ 1 ] 24523882-36777174 | [ 2 ] 12270589-24523881 |** [ 7 ] 17297-12270589 |************************************************** [ 175 ] Storage Throughput = excellent ( 1529.93 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40033805 bp ( 40030705 non ambiguous ) - Num Contigs Represented = 51 - Sequence extraction : 00:00:54 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:07:53 (hh:mm:ss) Elapsed Time Round Time: 00:15:28 (hh:mm:ss) Elapsed Time : 121 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:14 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:08 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 3724 repeats masked totaling 902287 bp(s). - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10003036 bp Num Contigs Represented = 28 Non ambiguous bp: Initial: 10002436 bp After Masking: 9044601 bp Masked: 9.58 % -- Input Database Coverage: 10003036 bp out of 966847183 bp ( 1.03 % ) Sampling Time: 00:00:25 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:03:08 (hh:mm:ss) Elapsed Time, 621 HSPs Collected Number of families returned by RECON: 244 Round Time: 00:03:38 (hh:mm:ss) Elapsed Time : 2 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:40 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:44 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 11485 repeats masked totaling 2806201 bp(s). - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30030689 bp Num Contigs Represented = 49 Non ambiguous bp: Initial: 30028189 bp After Masking: 26748817 bp Masked: 10.92 % -- Input Database Coverage: 40033725 bp out of 966847183 bp ( 4.14 % ) Sampling Time: 00:01:31 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283881 Comparison Time: 00:15:36 (hh:mm:ss) Elapsed Time, 5117 HSPs Collected Number of families returned by RECON: 1579 Round Time: 00:17:16 (hh:mm:ss) Elapsed Time : 6 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:03 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:35 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 34169 repeats masked totaling 8220007 bp(s). - TE Masking time 00:00:18 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90024128 bp Num Contigs Represented = 59 Non ambiguous bp: Initial: 90018728 bp After Masking: 80586756 bp Masked: 10.48 % -- Input Database Coverage: 130057853 bp out of 966847183 bp ( 13.45 % ) Sampling Time: 00:04:59 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2545896 Comparison Time: 01:45:21 (hh:mm:ss) Elapsed Time, 36898 HSPs Collected Number of families returned by RECON: 9570 Round Time: 01:51:19 (hh:mm:ss) Elapsed Time : 57 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:06:10 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:43 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 111912 repeats masked totaling 26872016 bp(s). - TE Masking time 00:01:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270054851 bp Num Contigs Represented = 106 Non ambiguous bp: Initial: 270036051 bp After Masking: 239611373 bp Masked: 11.27 % -- Input Database Coverage: 400112704 bp out of 966847183 bp ( 41.38 % ) Sampling Time: 00:13:12 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22980810 Comparison Time: 13:26:19 (hh:mm:ss) Elapsed Time, 224513 HSPs Collected Number of families returned by RECON: 65168 Round Time: 14:00:48 (hh:mm:ss) Elapsed Time : 228 families discovered. RepeatScout/RECON discovery complete: 414 families found Classification Time: 00:17:09 (hh:mm:ss) Elapsed Time Program Time: 16:45:38 (hh:mm:ss) Elapsed Time